editorialbot commented 1 year ago

Submitting author: !--author-handle-->@PetervanLunteren@mstimberg<!--end-editor-- Reviewers: @animikhaich, @oparisot Archive: 10.5281/zenodo.7223363

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/dabe3753aae2692d9908166a7ce80e6e/status.svg)](https://joss.theoj.org/papers/dabe3753aae2692d9908166a7ce80e6e)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@animikhaich & @oparisot, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @mstimberg know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @animikhaich

📝 Checklist for @oparisot

editorialbot commented 1 year ago

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@editorialbot generate pdf

editorialbot commented 1 year ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.04 s (414.2 files/s, 133953.8 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
Python                            1            437            509           2464
Bourne Again Shell                4            165            242            746
DOS Batch                         3             64              0            396
Markdown                          5             53              0            232
TeX                               1             10              0            136
YAML                              3              3              7             34
--------------------------------------------------------------------------------
SUM:                             17            732            758           4008
--------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 1 year ago

Wordcount for paper.md is 580

editorialbot commented 1 year ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1002/ece3.5767 is OK
- 10.1073/pnas.1922686117 is OK
- 10.1109/crv.2018.00052 is OK
- 10.1016/j.ecoinf.2017.07.004 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 1 year ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

mstimberg commented 1 year ago

👋🏼 @PetervanLunteren, @animikhaich, @oparisot, this is the review thread for the paper. All of our communications will happen here from now on.

As a reviewer, the first step is to create a checklist for your review by entering

@editorialbot generate my checklist

as the top of a new comment in this thread.

There are additional guidelines in the message at the start of this issue.

Please don't hesitate to ping me (@mstimberg) if you have any questions/concerns.

mstimberg commented 1 year ago

:wave: @animikhaich, @oparisot, no rush for performing the actual review of course, but just checking in to see whether there are any questions on your side or whether there's anything else I can do to help you with the review? Please be reminded that JOSS reviews can be iterative, i.e. feel free to open issues or comment here as soon as you come across concerns – there is no need to gather everything into a single review text as commonly done for traditional journals. In the same vein, please feel free to tick boxes in your checklist whenever you are sure about them (the two in the beginning – conflict of interest and code of conduct – would be good first candidates :wink: ). Thank you for your time :pray: !

animikhaich commented 1 year ago

Hi @mstimberg, Thanks for your message.

Apologies for the delay. I had a medical situation over the past two weeks and went through a major surgery. I am in recovery and should be able to initiate the review by the end of this week.

mstimberg commented 1 year ago

@animikhaich Sorry to hear about your medical issues, thank you for taking the time to reply. It goes without saying that getting well again should be your priority, not this review, so please don't feel pressured to finish it any time soon. We are grateful for your time in either case, and I am sure the authors understand that sometimes more important things get into the way. Also, please don't hesitate to contact me directly (marcel.stimberg@inserm.fr) in case you want to discuss things you might not be comfortable sharing in a public GitHub issue. Thanks again for your time and for replying, get well soon :pray: .

PetervanLunteren commented 1 year ago

@mstimberg @animikhaich Yes of course, it goes without saying that I completely understand. There is no rush!

animikhaich commented 1 year ago

Review checklist for @animikhaich

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/PetervanLunteren/EcoAssist?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@PetervanLunteren) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[ ] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

mstimberg commented 1 year ago

:wave: @oparisot did you have the time to look at the EcoAssist software/paper yet?

oparisot commented 1 year ago

Review checklist for @oparisot

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/PetervanLunteren/EcoAssist?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@PetervanLunteren) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[ ] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

oparisot commented 1 year ago

@mstimberg Hello, this software is really interesting!

PetervanLunteren commented 1 year ago

@mstimberg @animikhaich @oparisot Thanks for your time! I'm not too familiar with the review process. Are the unchecked boxes areas where the software performs poorly? In other words, are the unchecked boxes actions for me to revise?

mstimberg commented 1 year ago

@PetervanLunteren Unchecked boxes could mean that there is something to improve in the software/paper, but in that case the reviewers would either leave more specific comments here or open issues in your repository. In this case, it most likely simply means that the reviewers did not yet have the time to verify the unchecked criteria in detail.

oparisot commented 1 year ago

Hello @PetervanLunteren !!

I checked again the list -- I forgot to check two points, my review is up to date now. My general feedback: a great work, congrats for this software!

Two minor points:

Maybe I'm wrong, but I dont' see automated tests in the git repo. Can you confirm?
Are there similar software? If yes, what is the difference with EcoAssist?

Olivier

animikhaich commented 1 year ago

Hi @PetervanLunteren,

My checklist is updated. There is an error that is preventing me from running the standard test case and moving forward. I've opened an issue here. Please address the same and let me know if you need anything else.

A couple of points that need to be addressed:

The repository is missing a CONTRIBUTING.md file, which is required for the "Community Guidelines" checklist. You can refer to PyTorch's CONTRIBUTING.md as a reference on how to create one.
While not necessary, I recommend you containerize the program and add a Dockerfile to prevent installation/platform-based limitations like the issue I opened up. It also allows users to install and use the software without installing dependencies on the native system. You can learn more about Docker here. Further, you can also host your container on Docker Hub, which will allow users to simply download and run the container instead of having to build the container locally.

Best, Animikh

PetervanLunteren commented 1 year ago

Hi @oparisot, Thanks very much for your time! Please see my responses below.

Maybe I'm wrong, but I dont' see automated tests in the git repo. Can you confirm?

Indeed, there are currently no automated tests available. I have included documented manual steps for this purpose. I thought/hoped this to be sufficient for the JOSS review criteria, but if not: let me know. In that case I'll revise.

Are there similar software? If yes, what is the difference with EcoAssist?

Yes, there are similar packages available. I briefly discuss them in the paper (line 36-40). Do you advise me to expand on this?

Thanks, Peter

oparisot commented 1 year ago

Hello @PetervanLunteren ,

Ok for me for the tests, the documentation is sufficient. About similar packages, I just suggest to add a short sentence into the README file -- it's a Nice To Have.

Olivier

PetervanLunteren commented 1 year ago

About similar packages, I just suggest to add a short sentence into the README file -- it's a Nice To Have.

Thanks for the tip, I've added a section to the documentation: https://github.com/PetervanLunteren/EcoAssist#similar-software

Peter

PetervanLunteren commented 1 year ago

Hi @animikhaich, thanks for your time and suggestions! I'll respond to them below.

There is an error that is preventing me from running the standard test case and moving forward. I've opened an issue here. Please address the same and let me know if you need anything else.

Thanks for opening this issue and providing the detailed information. I've looked into it and it seems that it is not directly an EcoAssist issue, but rather a MegaDetector issue regarding the CUDA software that comes with the MegaDetector installation. I've opened an issue at the relevant repository and hope to resolve your problem together with the developers there. Any further communication about this will happen in the issue https://github.com/PetervanLunteren/EcoAssist/issues/16.

The repository is missing a CONTRIBUTING.md file, which is required for the "Community Guidelines" checklist. You can refer to PyTorch's CONTRIBUTING.md as a reference on how to create one.

Thanks for letting me know. Please see the updated repository, where I've updated the documentation and added a CONTRIBUTING.md and CODE_OF_CONDUCT.md.

While not necessary, I recommend you containerize the program and add a Dockerfile to prevent installation/platform-based limitations like the issue I opened up. It also allows users to install and use the software without installing dependencies on the native system. You can learn more about Docker here. Further, you can also host your container on Docker Hub, which will allow users to simply download and run the container instead of having to build the container locally.

This does indeed look great! I will look into this to make the installation more robust. However, since containerizing the program does ask for quite some time investment and the moment I do not have much spare time, I can't promise an ETA. Since it is not necessary for the JOSS publication, I'll add it to my TODO list and will look into it when time permits. I really appreciate the tip!

animikhaich commented 1 year ago

@PetervanLunteren, Thanks for addressing the issues. I've updated the checklist based on the CONTRIBUTING guidelines.

Since I cannot test the code on my GPU system due to the CUDA Error, I'll test it out on my Macbook and update the checklist based on the same.

animikhaich commented 1 year ago

@mstimberg Review Complete from my end. All issues have been addressed. Thanks @PetervanLunteren for the prompt response.

Please let me know if anything else is needed.

PetervanLunteren commented 1 year ago

@mstimberg for traceability, issue https://github.com/PetervanLunteren/EcoAssist/issues/16 opened by @animikhaich is now resolved with commit https://github.com/PetervanLunteren/EcoAssist/commit/bac8597ecf8623b339467b71864a27d34462e13e

@animikhaich @oparisot thank you very much for your valuable insights!

mstimberg commented 1 year ago

@oparisot your checklist still has a few boxes unchecked – are you still verifying things or would be happy for the paper/software to be published as it is?

@animikhaich if you recommend the publication of the paper/software in its current state, then there is nothing more to do from your side, I will take over for the final steps of the publication process :pray:

animikhaich commented 1 year ago

@mstimberg, Yes. The author has done extensive work and the tool does add value to the open-source community. Hence, I recommend moving forward with the publication. Thanks!

oparisot commented 1 year ago

@mstimberg Nice work of author -- it)' ok for me!

mstimberg commented 1 year ago

Great, thanks again for your time @animikhaich and @oparisot. With both reviewers recommending acceptance, I will now have a look over things myself and then perform the final necessary steps before publication.

mstimberg commented 1 year ago

@editorialbot generate post-review checklist

editorialbot commented 1 year ago

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

mstimberg commented 1 year ago

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

[x] Double check authors and affiliations (including ORCIDs)
[x] Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
[x] Archive the release on Zenodo/figshare/etc and post the DOI here.
[x] Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
[x] Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

[x] Read the text of the paper and offer comments/corrections (as either a list or a PR)
[x] Check the references in the paper for corrections (e.g. capitalization)
[x] Check that the archive title, author list, version tag, and the license are correct
[x] Set archive DOI with @editorialbot set <DOI here> as archive
[x] Set version with @editorialbot set <version here> as version
[x] Double check rendering of paper with @editorialbot generate pdf
[x] Specifically check the references with @editorialbot check references and ask author(s) to update as needed
[x] Recommend acceptance with @editorialbot recommend-accept

mstimberg commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1002/ece3.5767 is OK
- 10.1073/pnas.1922686117 is OK
- 10.1109/crv.2018.00052 is OK
- 10.1016/j.ecoinf.2017.07.004 is OK

MISSING DOIs

- None

INVALID DOIs

- None

mstimberg commented 1 year ago

@PetervanLunteren All looks very good to me, I only open a small PR fixing two of the references.

Just to check: am I correct that the software itself did not change during the review process, i.e. version v4.0 and the Zenodo archive at https://doi.org/10.5281/zenodo.7223363 are still the most recent ones?

PetervanLunteren commented 1 year ago

@mstimberg Yes, that is correct. Those are the latest versions.

mstimberg commented 1 year ago

@editorialbot set 10.5281/zenodo.7223363 as archive

editorialbot commented 1 year ago

Done! archive is now 10.5281/zenodo.7223363

mstimberg commented 1 year ago

Could you please manually fix some of the metadata in the Zenodo archive (no need to to a new tag/release)? In general, we prefer to have the archive metadata to be as consistent as possible with the JOSS paper. In particular, could you make the titles and author lists match? If you want to leave @ehallein in the author list on the Zenodo archive for completeness, that would be fine as well. Also, could you please:

add your ORCID on Zenodo
chose the correct license

If you want to make sure that this information will be correctly filled out in the feature when using the automatic GitHub-Zenodo bridge, you can specify them in a .zenodo.json file (https://developers.zenodo.org/?python#github).

PetervanLunteren commented 1 year ago

I've manually adjusted the details on Zenodo. Could you check if this is sufficient?

mstimberg commented 1 year ago

I've manually adjusted the details on Zenodo. Could you check if this is sufficient?

All good now :+1:

mstimberg commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

mstimberg commented 1 year ago

Excellent work everyone, thanks again @PetervanLunteren for choosing to publish with JOSS, and @animikhaich and @oparisot for taking the time to review the software. I will now recommend acceptance and trigger the final steps in the publication process (after confirmation by an editor-in-chief) :tada: .

mstimberg commented 1 year ago

@editorialbot recommend-accept

editorialbot commented 1 year ago

Attempting dry run of processing paper acceptance...

editorialbot commented 1 year ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1002/ece3.5767 is OK
- 10.1073/pnas.1922686117 is OK
- 10.1038/s41467-022-27980-y is OK
- 10.1109/crv.2018.00052 is OK
- 10.1016/j.ecoinf.2017.07.004 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 1 year ago

:wave: @openjournals/dsais-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/4444, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

PetervanLunteren commented 1 year ago

@mstimberg @animikhaich @oparisot thank you very much for your time!

oparisot commented 1 year ago

@PetervanLunteren you're welcome!

openjournals / joss-reviews

[REVIEW]: EcoAssist: A no-code platform to train and deploy custom YOLOv5 object detection models #5581

Status

Reviewer instructions & questions

Checklists

Review checklist for @animikhaich

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @oparisot

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance